TOol for Motif TO Motif comparison (TOMTOM)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use TOMTOM in your research, please cite the following paper:
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.

Query Motifs  |  Target Databases  |  Matches  |  Program information  |  Explanation

Query Motifs

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Name 

Preview 

Matches 

List 

1_e_k4me1-npc_0.549
CACAAAAGG
0
2_e_k4me1-h1_0.542
CCACCTGGG
0
3_h_k4me1-npc_0.539
ACAAAGGC
0
4_e_k4me1-h1_0.539
ACTACTACTC
0
5_e_k4me1-h1_0.539
CCCCACCCCT
12 ALFIN1_Q2_M00479_T,  SP1_Q2_01_M00933_T,  SP1_02_M01303_T,  ZFP281_01_M01597_T,  GC-box_POL003.1_J,  GC_01_M00255_T,  SP1_Q4_01_M00932_T,  SP1_MA0079.2_J,  SP1_Q6_01_M00931_T,  SP4_Q5_M01273_T
6_e_k4me1-h1_0.538
AATATCACC
0
7_e_k4me1-npc_0.538
AAGAAAGGC
0
8_h_k4me1-npc_0.537
GCAGCTCT
0
9_e_k4me1-h1_0.536
TACCACCCA
1 TRA1_02_M01049_T
10_e_k4me1-npc_0.535
AGCAAAGCC
0
11_h_k4me1-npc_0.534
AGAGGCCCTTGG
0
12_e_k4me1-h1_0.533
CGCAGGTATA
0
13_h_k4me1-npc_0.532
CTGACAGCCG
0
14_e_k4me1-npc_0.532
ACAATAGGG
0
15_e_k4me1-npc_0.531
CAGAAGCCA
0
16_e_k4me1-npc_0.531
ATCGTTTAAT
0
17_e_k4me1-h1_0.531
ATGTAAATG
0
18_e_k4me1-npc_0.530
CAGCACAGAG
0
19_h_k4me1-npc_0.528
CCCCTTTCAG
0
20_e_k4me1-h1_0.528
ATGTTGTA
0
21_e_k4me1-h1_0.528
AGTACTAC
0
22_e_k4me1-npc_0.527
AAGGAGACG
0
23_e_k4me1-h1_0.527
AAATGCAAAG
1 OCT1_Q6_M00195_T
24_h_k4me1-npc_0.527
TCCGTGGTTA
0
25_e_k4me1-npc_0.527
AGAGGCAGC
0
26_e_k4me1-npc_0.526
ACGGAGCC
0
27_e_k4me1-npc_0.524
AAGCAGCAC
0
28_e_k4me1-h1_0.524
ATATTCGGC
0
29_e_k4me1-h1_0.524
GTGAGTATC
0
30_e_k4me1-npc_0.521
AAAGACGTC
0
31_e_k4me1-h1_0.521
TGATATGCA
1 Pou5f1_MA0142.1_J
32_e_k4me1-h1_0.520
GATTCTACCA
0
33_e_k4me1-h1_0.520
CATTTACTGA
0
34_e_k4me1-npc_0.519
CACTGACGA
0
35_h_k4me1-npc_0.519
TGTGTACG
0
36_e_k4me1-npc_0.518
CCTTCAACAT
0
37_e_k4me1-npc_0.517
GATAAACAG
0
38_e_k4me1-npc_0.517
AGCGTGTCA
0
39_e_k4me1-npc_0.516
GAGCTCATC
0
40_e_k4me1-h1_0.515
CTTGGCCCA
0

Target Databases

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Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiCmbned3.meme 2921 15

Matches to Query: 1_e_k4me1-npc_0.549

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Matches to Query: 2_e_k4me1-h1_0.542

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Matches to Query: 3_h_k4me1-npc_0.539

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Matches to Query: 4_e_k4me1-h1_0.539

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Matches to Query: 5_e_k4me1-h1_0.539

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Summary 

Alignment 

Name ALFIN1_Q2_M00479_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.3898e-06
E-value 0.0040596
q-value 0.00461781
Overlap 10
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name SP1_Q2_01_M00933_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.92313e-06
E-value 0.00561748
q-value 0.00461781
Overlap 10
Offset 0
Orientation Normal
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Summary 

Alignment 

Name SP1_02_M01303_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 2.39433e-06
E-value 0.00699384
q-value 0.00461781
Overlap 9
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name ZFP281_01_M01597_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 4.2775e-06
E-value 0.0124946
q-value 0.00602307
Overlap 10
Offset 0
Orientation Reverse Complement
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Summary 

Alignment 

Name GC-box_POL003.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.12356e-06
E-value 0.0208079
q-value 0.00602307
Overlap 10
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name GC_01_M00255_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 7.12356e-06
E-value 0.0208079
q-value 0.00602307
Overlap 10
Offset 3
Orientation Reverse Complement
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Summary 

Alignment 

Name SP1_Q4_01_M00932_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.44361e-06
E-value 0.0275848
q-value 0.00602307
Overlap 10
Offset 2
Orientation Reverse Complement
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Summary 

Alignment 

Name SP1_MA0079.2_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 9.94668e-06
E-value 0.0290542
q-value 0.00602307
Overlap 10
Offset 0
Orientation Normal
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Summary 

Alignment 

Name SP1_Q6_01_M00931_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.07096e-05
E-value 0.0312827
q-value 0.00602307
Overlap 9
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name SP4_Q5_M01273_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.0747e-05
E-value 0.031392
q-value 0.00602307
Overlap 10
Offset 1
Orientation Normal
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Summary 

Alignment 

Name UF1H3BETA_Q6_M01068_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.14508e-05
E-value 0.0334479
q-value 0.00602307
Overlap 10
Offset 1
Orientation Reverse Complement
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Summary 

Alignment 

Name YPR022C_01_M01647_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.47198e-05
E-value 0.0429965
q-value 0.0070973
Overlap 6
Offset 0
Orientation Normal
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Matches to Query: 6_e_k4me1-h1_0.538

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Matches to Query: 7_e_k4me1-npc_0.538

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Matches to Query: 8_h_k4me1-npc_0.537

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Matches to Query: 9_e_k4me1-h1_0.536

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Summary 

Alignment 

Name TRA1_02_M01049_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 6.55821e-06
E-value 0.0191565
q-value 0.0383078
Overlap 8
Offset -1
Orientation Reverse Complement
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Matches to Query: 10_e_k4me1-npc_0.535

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Matches to Query: 11_h_k4me1-npc_0.534

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Matches to Query: 12_e_k4me1-h1_0.533

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Matches to Query: 13_h_k4me1-npc_0.532

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Matches to Query: 14_e_k4me1-npc_0.532

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Matches to Query: 15_e_k4me1-npc_0.531

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Matches to Query: 16_e_k4me1-npc_0.531

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Matches to Query: 17_e_k4me1-h1_0.531

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Matches to Query: 18_e_k4me1-npc_0.530

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Matches to Query: 19_h_k4me1-npc_0.528

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Matches to Query: 20_e_k4me1-h1_0.528

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Matches to Query: 21_e_k4me1-h1_0.528

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Matches to Query: 22_e_k4me1-npc_0.527

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Matches to Query: 23_e_k4me1-h1_0.527

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Summary 

Alignment 

Name OCT1_Q6_M00195_T
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 1.53397e-05
E-value 0.0448072
q-value 0.0832066
Overlap 10
Offset 2
Orientation Normal
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Matches to Query: 24_h_k4me1-npc_0.527

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Matches to Query: 25_e_k4me1-npc_0.527

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Matches to Query: 26_e_k4me1-npc_0.526

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Matches to Query: 27_e_k4me1-npc_0.524

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Matches to Query: 28_e_k4me1-h1_0.524

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Matches to Query: 29_e_k4me1-h1_0.524

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Matches to Query: 30_e_k4me1-npc_0.521

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Matches to Query: 31_e_k4me1-h1_0.521

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Summary 

Alignment 

Name Pou5f1_MA0142.1_J
Database trnsfcJsprUnprobHpdiCmbned3.meme
p-value 8.93e-06
E-value 0.0260845
q-value 0.0521691
Overlap 9
Offset 3
Orientation Normal
Create custom LOGO ↧  [Query Top]

Matches to Query: 32_e_k4me1-h1_0.520

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Matches to Query: 33_e_k4me1-h1_0.520

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Matches to Query: 34_e_k4me1-npc_0.519

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Matches to Query: 35_h_k4me1-npc_0.519

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Matches to Query: 36_e_k4me1-npc_0.518

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Matches to Query: 37_e_k4me1-npc_0.517

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Matches to Query: 38_e_k4me1-npc_0.517

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Matches to Query: 39_e_k4me1-npc_0.516

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Matches to Query: 40_e_k4me1-h1_0.515

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TOMTOM version
4.8.1 (Release date: Tue Feb 7 14:03:40 EST 2012)
Reference
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.
Command line summary

Background letter frequencies (from first motif database):
A: 0.295   C: 0.205   G: 0.205   T: 0.295

Result calculation took 90.979 seconds
show model parameters...

Explanation of TOMTOM Results

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The TOMTOM results consist of

Inputs

The important inputs to TOMTOM.

Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name
The motif name.
Alt. Name
The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website
A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview
The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches
The number of significant matches.
List
Links to the first 20 matches
Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database
The database name.
Number of Motifs
The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched
The number of motifs that had a match with at least one of the query motifs.

Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

Summary Table

The summary gives the important statistics about the motif match.

Name
The name of the matched motif.
Alt. Name
The alternative name of the matched motif.
p-value
The probability that the match occurred by random chance according to the null model.
E-value
The expected number of false positives in the matches up to this point.
q-value
The minimum False Discovery Rate required to include the match.
Overlap
The number of letters that overlaped in the optimal alignment.
Offset
The offset of the query motif to the matched motif in the optimal alignment.
Orientation
The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.
Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type
Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars
Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC
Toggle adding pseudocounts for Small Sample Correction.
Flip
Toggle a full reverse complement of the alignment.
Width
Specify the width of the generated motif.
Height
Specify the height of the generated motif.